Müller wanted to go to Paris to study with Georges Cuvier (1769-1832), Europe’s leading comparative anatomist. Instead, the Bonn University Curator Philipp Jakob Rehfues granted him money to study with the Berlin anatomist Carl Asmund Rudolphi (1771-1832), who strongly criticized Naturphilosophie and advocated microscopic studies. Müller quickly became an adept microscopist, and when he passed his Prussian state medical exam and returned to Bonn in the winter of 1824, Rudolphi gave him his own Frauenhofer microscope to conduct his own research (Haberling 1924, p. 54). Müller remained in Bonn until 1833, rising from lecturer (1824) to Professor Extraordinarius (1826) to Professor Ordinarius (1830) and using the Frauenhofer instrument to perform an extraordinary number of physiological and anatomical studies.

On October 19, 1824, Müller delivered a lecture “Ueber das Bedürfnis der Physiologie nach einer philosophischen Naturbetrachtung” (On the Need of Physiology for a Philosophical Contemplation of Nature) in which he outlined a scientific strategy he would use for much of his life, combining close observation of natural forms with limited philosophical theorizing about their interrelations (Rothschuh 1973, p. 197). The question of whether Müller developed his comparative anatomy and physiology out of or in opposition to Naturphilosophie has raised considerable controversy (Hagner and Wahrig-Schmidt 1992). Müller opposed both empty theorizing and blind empiricism, advocating natural science based on close observation and philosophical pattern-seeking and systematization.